Models of virues (19th of October 2012)

We physicists tend to simplify the reality. In physics, it is not done for some "style" or "trend" but because the simplification aims to preserve that which is important, the essence of "reality", and separate it from the unimportant which can be reproduced as one wishes, once the essence is understood.

One could also say that this defines the "physical system", although this definition is somewhat stylistically and sociologically determined - the physical system is the system which can be simplified to the level where the physicists can explore it completely.

Well, I thought, and I still think, that viruses are such, physical systems. That is why I for some time already, together with my Slovenian colleagues, work on finding the common characteristics of all viruses. >> The paper we just published is on that trail, although the amount of universal characteristics of viruses is significantly smaller than we expected. But that is how the world is, and it needs to be "realistically" painted in this moment in time. After this paper, we can say that we do not completely understand the role of electrostatic interactions in viruses and their importance for the electrostatic "design" of capsid proteins and viral genome.

We used to, in our super-perfect-extra-simple physicists' world, view viruses usually as perfectly spherical (of course) distributions of charge in which the charge on the protein coating is distributed either on a single infinitely thin shell (the image above, left), or on two infinitely thin shells (image above, right) separated by the uncharged protein material.

The distribution of protein mass of a real virus ( >> cucumber mosaic virus) is shown on the image above. It is not exactly a sphere, but it is also not that different from a sphere. With respect to scientific illustration, here I, I think interestingly, combined 3D graphical representation (above) with the graph of mass distribution.

A similar visualization was used to show the distribution of positive (red) and negative (blue) charge in the protein coating, this time of simian 40 virus (above). This image shows that it is very difficult to see something special and recognizable in the distribution, something which would clearly be good "for something". In the case of simian 40 virus, one sees only a very patchy distribution which does not say much, at least not to me. Our simplified models obviously do not work for this virus, but they are better for some other viruses, e.g. for CMV virus (below). In this case, one observes that the inner surface of the protein coating is mostly positively charged, while the outer surface is mostly negative. This is a "common wisdom" one usually finds in the relevant literature, but our analysis shows that this feature is by no means universal for viruses.

A detailed analysis of virus structures deposited in PDB databases was performed by Anže Lošdorfer Božič. Read the results in the >> paper we just published.

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Last updated on 19th of October 2012.